Biomedicine (BM10010 Lecture Notes PDF

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BIOMEDICINE LECTURE NOTESWEEK 1LECTURE 1: EPIDEMIOLOGY OF INFECTIOUS DISEASE: PRINCIPLES OF INFECTIONCONTROL Key DefinitionsThe principle of infectious diseases are relationships and the following terms describe possible relationships, which can lead to the development of an infection.o Symbiosis: ...

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BIOMEDICINE LECTURE NOTES

WEEK 1 LECTURE 1: EPIDEMIOLOGY OF INFECTIOUS DISEASE: PRINCIPLES OF INFECTION CONTROL

 Key Definitions The principle of infectious diseases are relationships and the following terms describe possible relationships, which can lead to the development of an infection. o Symbiosis: living together (Note: that the relationship of living together may not a beneficial or harmful relationship) o Mutualism: two independent organisms living together and mutually benefitting from each other (this can be described as falling in love)

o Commensalism: this is the relationship where one benefits however, it doesn’t mean that the other individual is harmed or benefitted o Parasitism: one organisms lives at the expense of another (the relationship between children and parents can be described as parasitism, where the child benefits at the expense of the parents)

o Opportunism: where one benefits only when another organism is compromised, however under normal circumstances the benefiting organism would not be able to cause an infection (this can be known through the example of a boy getting dumped and thus being vulnerable and a girl only being attracted to him due to his vulnerability) o Communicable: one host to the other o Contagious: degree to which a disease is communicable o Non-communicable: non-human/animal spread o Endogenous infection: growing or originating from the organism o Exogenous: origin from another source

 Understanding: What are the principles of infectious disease?

In order to understand the how microbe causes a disease, it is important to note that the environment of both the host and microbe contribute to the manifestation of disease

The Microbe  

Have the ability to cause disease (pathogenicity) Virulence: the degree to which the microbe can cause harm ( usually refers to the speed at which they can cause harm or the amount of damage the microbe can do

The Environment

The Host 

Must be susceptible to infection. (Susceptibility refers to the geographical location, physiology etc.)

Must allow the microbe to survive and potentially reproduce  Must have the conditions to allow the microbe to infect the host (transmission

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Note: that in order for the microbe to cause a disease or an infection, it must be a parasite or a pathogen Therefore, a microbe, which is pathogen must be able to do four main things in order to cause a disease 1) Gain entry to the host o Reservoir of infection, which refers to the environment in which the pathogen lives and reproduces o Portal of entry and exit, which may be through the mouth, ear, nose or even sex organs o Mode of transmission, which may be through physical contact If the three principles of how a microbe can gain entry into the host are understood, then it is possible to implement control strategies 2) Attach and multiply 3) Evade host defences (refers to opportunism) 4) Cause damage to cells/tissue o Physical invasion/ disruption o Toxins

F

 How do we encounter microbes (modes of transmission)? 1) Humans: normal flora, which refers to human microbiota. Keep in mind that different people have different microbiota 2) Animals 3) Soil 4) Water/food 5) Air borne 6) Vectors: don’t infect the host itself, but rather spreads infection by conveying the pathogen from one host to the next. There are two types of vectors: (a) Mechanical: vectors who transmit infection, but the transmission of infection is not an essential part of their life cycle (b) Biological: transmission is part of their life cycle So, once we encounter microbes, how do they actually enter our body? Well, there various ways this can occur: 1) 2) 3) 4) 5)

Skin Respiratory tract: mouth, nose Gastrointestinal tract: route for food borne pathogens Urogenital: STD, Urinary tract infection Transplacental: some microbes and viruses, which primarily affect adults have the ability to cross the placenta and affect foetus

Note: note that the portal of exit are the same/ similar to the portal of entry or they are related to the organ system Note: any infection that become blood borne can in theory be passed through blood or bodily fluids

 How can we control the transmission of infection? The overarching ways to control the transmission of infection is: 1) 2) 3) 4) 5)

To break the transmission cycle Change host behaviour Eliminate vectors/ physical reduction in microbe populations Sanitation Barrier protection- portal of entry and exit

These 3 methods can be implemented physically or in a chemotherapeutic manner:

PHYSICAL MEANS

CHEMOTHERAPEUTIC

Sterilisation- complete elimination of life

Antibiotics

Disinfection- reduction to an “acceptable level”

Immunisations/Vaccines- which act as a form of hygiene

Antiseptics- a type of disinfectant that can be used on the skin without harming the skin or the mucous membrane

Antimicrobials

 What is it about healthcare facilities that encourage infection? “Infection is more likely acquired in a hospital than in the community” This statement can be analysed via the multiplier effect. Since the hospital accommodates the sick, it naturally increases the reservoir of infection and thus increases the opportunity of transmission. Moreover, hospitals tend to mostly accommodate the elderly or the young. Both of these audiences have a weak immune system. This therefore allows the pathogen to be successful in infecting the person and causing harm. Even though hospitals have higher usage of disinfectants and antibiotics, this just makes the environment more susceptible to pathogens as the weaker pathogens easily die, however the stronger pathogens survive and multiply. This creates a viscous cycle, which often leads to antibiotics resistance Infection rates are also higher because of the equipment used and bodily fluid samples such as blood.

 How do we reduce infection in the hospital environment? 1) Medical asepsis (a) Clean hospital (b) Short stay of patients (c) Do not over crowed hospitals (d) Appropriate hygiene, such as staff and patients immunisation (e) Sterile dressings/ aseptic procedures (f) Handwashing in between patients 2) Surgical asepsis (a) Sterilisation of instruments (b) Disinfected operating procedures (c) Barrier protection 3) Standard precautions (a) Staff protection through appropriate work practices (b) Knowledge of microbiology essential

4) Infection control committee (a) Education to healthcare professionals (b) Monitor resistance patterns and incidences WEEK 3 LECTURE: A PRIMER ON VENEPUNCTURE… WHAT CAN GO WRONG?

 Anatomy Arteries We don’t draw blood from arteries because they carry blood at a very high temperature and they have elastin, which makes the blood taking process painful and complicated. The only time we do take blood from the arteries is if we want to check acid-base levels or in the case of emergency, check if the patient is breathing. Arterial blood gas (ABG) is a blood test that is used to measure the pH levels of oxygen and carbon dioxide Blood is drawn from brachial artery

 Veins Venous valves Choice of veins:   

Cephalic vein Basilic vein Median cubital

Types of veins 

Prominent veins o Large prominent and they tend to be bouncy, these are the veins that we are aiming for

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Deep veins o These are good veins, which often lie below the skin surface o When trying to find them be guided by what you feel rather than what you see

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Thready veins o Once punctured they often bleed profusely and this means they need extra care with haemostasis o These type of veins are commonly found with people who have aged or are sick o If the blood is drawn using a severe vacuum these types of veins will collapse and become useless Superficial veins o Tiny veins which appear on the surface of the arm but they are generally not suited to venepuncture

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Floating veins

o These tend to “float” away and escape as you try and draw blood o Hence, before inserting the needle you need to anchor the vein below the intended puncture site with the thumb or forefinger ensuring that it doesn’t just float away 

Thrombosed veins o These veins have been subjected to over use from venepuncture or drug abuse o They are hard and knotty to touch

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Very deep veins o Often associated with obese patients

 Procedure of venepuncture 1. Hand washing 2. Putting on gloves 3. Checking 2 forms of ID with the patient: DOB and Name 4. Collecting all the necessary equipment 5. Tourniquet application 6. Feeling for the vein 7. Loosening tourniquet 8. Sterile alcohol wipe 9. Drawing the blood whilst making sure the bevel of the needle is pointing up 10. Following the correct order of draw 11. Explaining aftercare to patient 12. Sample mixing and labelling in front of patient Why do we wash our hands and sterilize the site of collection? This step eliminates or reduces pre-analytical variables and ensures that the blood results are not due to an artefact What is the purpose of the tourniquet?    

Reduced venous return Forces fluids into the tissues Concentration of proteins and cells in blood Changes in cell counts proteins and anything else bound to proteins

Note: only have the tourniquet on for 2 minutes at a time otherwise it can cause the release of substances such a s potassium, which can alter the blood samples and ultimately the results as well What type of alcohol wipes should we use? Alcohol wipes which contain isopropyl alcohol Betadine wipes contain iodine 

Causes of decreased phosphate o Lab error o Decreased absorption

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Post-prandial alkaline tide Enteral nutrition Miscellaneous

o Transcellular shift (intracellular and extracellular fluid exchange)  Respiratory alkalosis  Insulin or glucose administration  Hypothermia o Increased renal loss  Hyperparathyroidism  Renal disease  Osmotic diuresis  Inhibitors of renal absorption What are some reasons as to why we get unexpected results from blood sample? Stress or hyperventilation at the time of sample collection can cause that because you loose carbon dioxide

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Anticoagulants TYPE OF TUBE EDTA

FEATURES  

  Citrate

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Heparin

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Fluoride oxalate

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Chelates Ca2+ and other di valent metal ions It will remove metal ions and preserve the red blood cells Stops clotting Haematology Chelates Ca2+ and other di-valent metal ions Stops clotting Coagulation (semi solid or solid state) studies It is reversible Used for urgent chemistry (happy for the blood to clot) Activate anti-thrombins thus stopping clotting

Inhibits glycolysis glucose

IMAGE

Plain

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Chemistry

Gel separator

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Gel separates red cells from serum

Order of draw

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Venepuncture sites o Dorsal hand o Wrist veins o Forearm veins o Leg, ankle and foot veins

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Things to avoid o Veins that are fibrosed, inflamed or fragile o Bruised areas o Sites close to infection o Affected side of stroke (CVA) or mastectomy o Areas affected by disabling diseases

LECTURE: DISCIPLINES OF THE MEDICAL LABORATORY/ PATHOLOGY

 Describe the clinical utility of each discipline

Haematology is the study of the components of blood and coagulation. The types of diseases commonly studied in haematology: 

  

Anaemia o Lack of red cell mass o Lack of haemoglobin o Capacity for oxygen transport and utilisation is decreased Infection  White cells part of host defence mechanism Leukaemia  Cancer of blood cells Coagulopathy  Errors in clotting mechanism

The main components of blood      

Erythrocytes Leucocytes Platelets Plasma: fluid from unclotted sample Serum: fluid from clotted sample Coagulation proteins: not utilised in a clotting process

So how are the components of blood altered in pathology? 1) Quantitatively  Change in total numbers  Low erythrocytes o Anaemia  High leukocytes o Infection/ leukaemia 2) Qualitatively  Red cells: o Change in size: anisocytosis o Change in shape: poikilocytosis o Change in colour: polychromasia Red cell changes:

TYPE

CHARACTERISTIC

IMAGE

Normal Blood Film

Even distribution of red blood cells Area of central pallor: which is the white centre the blood cells have as shown in the image

Iron deficiency anaemia

Microcytes Anisocytosis Poikilocytosis Hypochromasia

B12 Folate deficiency

Macrocytes Nucleated red cells

Haemolytic anaemia

Spherocytes Polychromasia

How are these components altered? 3) Quantitatively  Change in total numbers  Low erythrocytes o Anaemia  High leukocytes

o Infection/ leukaemia 4) Qualitatively  White cells: o Maturation o Inclusion bodies/ staining characteristics White cell changes: TYPE

CHARACTERISTIC

Normal Film

Infection: sepsis

Immature forms Toxic changes Doehle’s bodies

Leukaemia

Genetic error in maturation Proliferation Bone marrow forms in PB

IMAGE

Platelet Changes

Normal

Platelet Changes

Large Small Hypo granular Decreased function: may not be morphological association

There five types of white cells each of which has a specific function o Neutrophils: bacterial infection o Lymphocytes: part of our immune defence and act to recognise antigens and produce antibodies o Monocytes: help other white blood cells remove dead or damaged tissues and destroy cancer cells and regulate immunity o Eosnophils: parasitic infection o Basophils: appear in specific kinds of inflammatory reactions

Basophil

Neutrophils Eosinophil

Lymphocyte

Reactive lymphocyte

Monocyte

 List the common tests conducted in discipline and determine what are the sample requirements for these tests 

Full blood count: o Determine the quantitative abnormalities. This can be done by cell counters and automation o Determine the qualitative abnormalities through the examination of blood film. o Sample requirements  Need cells available to quantify and cell morphology preserved  Whole blood  Ensure anticoagulated  Mixed well prior to analysis  Use anticoagulant that will preserve and not interfere with morphological integrity of cell structure o Recommendation: EDTA as it chelates Ca2+ and Mg2+ which are requirements for coagulation process o Problems: neutrophils are not preserved after 8 hours o After 1 day red cells begin deteriorating

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Coagulation Tests o Activated partial ThromoT/ PT o Plasma required to test the activity of coagulation pathway: which is activated and timed o Must ensure activity of protein is intact o Sample requirements  Plasma (unclotted)  Action must be reversible: EDTA is not  Sodium citrate is used because action is reversible and able to determine the activity of coagulation process

LECTURE: INTRODUCTION TO LABORATORY QUALITY AND PRE-ANALYTICAL ERROR

 Review sample theory and the laboratory Med lab scientists are responsible for identifying pathology and providing evidence for pathology. In order for a patient to be correctly diagnosed the lab is responsible for ensuring that the evidence is accurate, precise and reproducible

So how do ensure the quality of evidence? Evidence in most cases is collected through the analysis of clinical sample and as scientists we hope that the clinical sample reflects the population as a whole whilst representing the specific condition of the patient. However, we as med lab scientists have to understand the consequences of this. So what sort of things do we analyse when trying to identify the cause of a disease? We can look for specific compounds or elements that our body uses and changes in their concentration which can possibly induce disease, their microbiology and perhaps identifying a foreign organism by identifying their unique genome in our system or we can also use antigen as marker for disease Example: Diabetes, which is problem with glucose tolerance/ metabolism and the glucose concentration acts the marker for high or low concentration The blood sample collected for analysis must reflect the patient condition, however the glucose concentration can be altered if the blood sample is stored in an anti-coagulant tube because it will start using the environmental glucose. This demonstrates how we cannot rely on the concentration in the sample to reflect on the concentration of a compound in the patient’s body as a whole Solution: use fluoride oxalate for blood collection Example: Hepatitis B Why is quality of evidence important? 1. Patient outcome - Length of bed stay - Duration and success of treatment 2. Public health - Community well being 3. Disease control - Control and monitoring of outbreaks 4. Health planning - Future directions in research and resource allocation  Review lab work flow Three phases: -

Pre- analytical Analytical Post-analytical

If there are errors in any of these phases the quality of care is threatened

 Identify pre-analytical variables and determine how they can be controlled  Pre-analytical phase o Sample collection/ test utilisation  The right sample for the job  Sample integrity vital for quality outcome  Storage and transport to lab o Lab may be directly responsible for activity

 

But must control this phase and recognise its impact on analysis Requires close association with users of lab services

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Analytical o Laboratory phase o Skilled people o Good/safe working conditions o Appropriate technology (cost/benefit) o Accuracy, precision, reproducibility

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Post analytical o Post laboratory o Results generation: communication to users o Result interpretation

Three categories of pre-analytical variation (sample error) A. Pre- collection causes - Cyclic biological variation: natural variation of elements and compounds in our body overtime. Hence, we have to ensure that the variation in the results is not due to our body’s natural processes but actually a possible disease  Examples of variation: circadian (change on a daily basis), ultradian (change in bursts, typically as result of a stimuli), infradian (happen over a long period), circannual (seasonal)  Example of infradian: female menstruation cycle  Example of circadian: urinary chemistry can dramatically change during a small period of time  Example of circannual: seasonal fruits and vegetables can change the concentrations of certain elements in our body  Example of ultradian: hormones which are used to digest food  Possible solutions:  Standard collection times  Collect over 24 hours  Report outcome of isolated result with caution - Patient relates variation  Exercise induces cell damage and heightened metabolism o Cell damage  Intracellular enzymes  CK and liver function tests o Heightened metabolism  Urea, lactic and uric acid up  Glucose and reproductive hormones down  Diet o Post prandial increase  Glucose  Triglyceride  Iron o Post prandial decrease

 Potassium  Phosphate o Stress  Cortisol and some other hormones  Flight and fight response o Posture  Postural hypotension  Blood pressure when standing up and low when standing down o Possible solutions:  Patient ...